R Notebook

Here we want to intersect the proteins identified in the 4 experiments we will publish: 1. 3 reps 400mJ/cm2 254nm UVC SILAC 2. TMT RNAse experiment 3. TMT dosage experiment 4. Cell cycle experiment

source("../../../R/Utility.R")
source("../../../R/Enrichment.R")

data.table 1.10.4.3
  The fastest way to learn (by data.table authors): https://www.datacamp.com/courses/data-analysis-the-data-table-way
  Documentation: ?data.table, example(data.table) and browseVignettes("data.table")
  Release notes, videos and slides: http://r-datatable.com

Attaching package: ‘data.table’

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Loading required package: BiasedUrn
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library("Biobase")
#source("https://bioconductor.org/biocLite.R")
#biocLite("MSnbase")

single_classification_df <- readRDS("../../../dLOPIT/pilot/notebooks/analysis/hyperLOPIT_Classifications.rds")
write.table(single_classification_df, "../../../dLOPIT/pilot/notebooks/analysis/hyperLOPIT_Classifications.tsv",
            sep="\t", quote=F)

SILAC_df <- read.table("../../trizol_dosage/analysis/data_processing/enriched_proteins.tsv", sep="\t", header=TRUE)
SILAC_df <- SILAC_df[SILAC_df$dosage==400,]
print(length(unique(SILAC_df$master_protein)))

[1] 773

TMT_RNAse_df <- readRDS("../../TMT_4_step_3_step/notebooks/protein_quantification.Rds")

Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 2.4.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

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print(head(data.frame(exprs(TMT_RNAse_df))))

print(length(rownames(exprs(TMT_RNAse_df))))

[1] 2540

TMT_dosage_df <- readRDS("../../TMT_4_step_dosage/analysis//protein_quantification.Rds")
print(head(data.frame(exprs(TMT_dosage_df))))

print(length(rownames(exprs(TMT_dosage_df))))

[1] 1505

TMT_dosage_repeat_df <- readRDS("../../TMT_4_step_dosage_repeat/analysis//protein_quantification.Rds")
print(head(data.frame(exprs(TMT_dosage_repeat_df))))

print(length(rownames(exprs(TMT_dosage_repeat_df))))

[1] 2116

TMT_cell_cycle <- readRDS("../../cell_cycle/data/rpb_res_pro_agg_norm_impute.rds")
print(head(data.frame(exprs(TMT_cell_cycle))))

print(length(rownames(exprs(TMT_cell_cycle))))

[1] 2198

SILAC_proteins <- as.character(unique(SILAC_df$master_protein))
TMT_RNAse_proteins <- as.character(rownames(exprs(TMT_RNAse_df)))
TMT_dosage_proteins <- as.character(rownames(exprs(TMT_dosage_df)))
TMT_dosage_rep_proteins <- as.character(rownames(exprs(TMT_dosage_repeat_df)))
TMT_cell_cycle_proteins <- as.character(rownames(exprs(TMT_cell_cycle)))
#all_proteins <- Reduce(union, list(SILAC_proteins, TMT_RNAse_proteins, TMT_dosage_proteins,
#                                   TMT_dosage_rep_proteins, TMT_cell_cycle_proteins))
#cat_proteins <- c(SILAC_proteins, TMT_RNAse_proteins, TMT_dosage_proteins,
#                  TMT_dosage_rep_proteins, TMT_cell_cycle_proteins)
#all_proteins <- Reduce(union, list(SILAC_proteins, TMT_RNAse_proteins,
#                                   TMT_dosage_rep_proteins, TMT_cell_cycle_proteins))
all_proteins <- Reduce(union, list(TMT_RNAse_proteins,
                                   TMT_dosage_rep_proteins, TMT_cell_cycle_proteins))
#cat_proteins <- c(SILAC_proteins, TMT_RNAse_proteins, TMT_dosage_rep_proteins, TMT_cell_cycle_proteins)
cat_proteins <- c(TMT_RNAse_proteins, TMT_dosage_rep_proteins, TMT_cell_cycle_proteins)
print(length(all_proteins))

[1] 3019

protein_counts <- table(as.character(cat_proteins))
plot(hist(protein_counts))

print(length(protein_counts[protein_counts>1]))

[1] 2193

seen_once_proteins <- names(protein_counts[protein_counts==1])
seen_proteins <- names(protein_counts[protein_counts>0])
seen_twice_proteins <- names(protein_counts[protein_counts>1])
seen_three_proteins <- names(protein_counts[protein_counts==3])
seen_all_proteins <- names(protein_counts[protein_counts==3]) # the same as above now SILAC excluded

print('P25054' %in% cat_proteins) # APC

[1] TRUE

print('Q15717' %in% cat_proteins) # ELAV1/HuR

[1] TRUE

print(protein_counts[names(protein_counts)=='P25054'])

P25054 
     2 

print(protein_counts[names(protein_counts)=='Q15717'])

Q15717 
     3 

data.frame(protein_counts)

write.table(protein_counts, "protein_counts.tsv", sep="\t", quote=F, row.names=F)

go_RNA_binding_inf <- "../../../shared_files/uniprot_go/uniprot_go_RNA_binding.tsv"
glycoproteins_inf <- "../../../shared_files/glycoproteins.tsv"
signal_peptides_inf <- "../../../shared_files/signal_peptides.tsv"
go_RNA_binding_df <- read.table(go_RNA_binding_inf, sep="\t", header=T)
glycoproteins_df <- read.table(glycoproteins_inf, sep="\t", header=T)
signal_peptides_df <- read.table(signal_peptides_inf, sep="\t", header=T)
geiger_df <- read.csv("../../../shared_files/Geiger_et_al/Geiger_et_al_2012_U2OS_peptides_plus_master.tsv",
                      header=TRUE, sep="\t")
print(length(unique(geiger_df$master_protein)))

[1] 9463

geiger_df <- geiger_df[geiger_df$unique==1,]
print(length(unique(geiger_df$master_protein)))

[1] 7455

geiger_df <- geiger_df[geiger_df$master_protein!="",]
print(length(unique(geiger_df$master_protein)))

[1] 7454

geiger_df <- geiger_df[geiger_df$crap_protein==0,]
print(length(unique(geiger_df$master_protein)))

[1] 7454

geiger_df <- geiger_df[geiger_df$associated_crap_protein==0,]
print(length(unique(geiger_df$master_protein)))

[1] 7454

agg_geiger_max <- aggregate(list(geiger_df$Max, as.numeric(as.character(geiger_df$protein_length))),
                            by=list(geiger_df$master_protein), FUN=mean)
colnames(agg_geiger_max) <- c("master_protein", "Max", "Length")
agg_geiger_max$log_length <- log(agg_geiger_max$Length, 2)
agg_geiger_max$norm_log_length <- normrank(agg_geiger_max$log_length)
agg_geiger_max$norm_abundance <- normrank(agg_geiger_max$Max)
agg_geiger_max$harm_mean_bias <- apply(agg_geiger_max[,c("norm_log_length", "norm_abundance")], MARGIN =1, FUN=harm_mean)
agg_geiger_max <- merge(agg_geiger_max, data.frame(protein_counts),
                        by.x="master_protein", by.y="Var1", all.x=TRUE)
agg_geiger_max$Freq[is.na(agg_geiger_max$Freq)] <- 0
agg_geiger_max <- merge(agg_geiger_max, single_classification_df[,c("Accession", "svm", "svm.scores")],
                        by.x="master_protein", by.y="Accession", all.x=TRUE)
geiger_u2os_proteins <- unique(agg_geiger_max$master_protein)
RBPs <- unique(go_RNA_binding_df$Entry)
glycoproteins <- unique(glycoproteins_df$protein)
makeVennPlot(seen_once_proteins, RBPs, glycoproteins, subset_to=geiger_u2os_proteins)

makeVennPlot(seen_twice_proteins, RBPs, glycoproteins, subset_to=geiger_u2os_proteins)

makeVennPlot(seen_three_proteins, RBPs, glycoproteins, subset_to=geiger_u2os_proteins)

makeVennPlot(seen_all_proteins, RBPs, glycoproteins, subset_to=geiger_u2os_proteins)

qm <- myProtMapper(union(all_proteins, unique(agg_geiger_max$master_protein)))

Querying chunk 1
Querying chunk 2
Querying chunk 3
Querying chunk 4
Querying chunk 5
Querying chunk 6
Querying chunk 7
Querying chunk 8

Finished
Pass returnall=TRUE to return lists of duplicate or missing query terms.
[1] "No KEGG"

the condition has length > 1 and only the first element will be used

# Mapping Uniprot to GO or Uniprot to Interpro for goseq
uniprot.go <- makeGene2Cat(qm,"query","go.all",";")
polyA_binding <- uniprot.go[uniprot.go$to.id=="GO:0008143", "query"]

makeVennPlot(TMT_RNAse_proteins, TMT_dosage_rep_proteins, TMT_cell_cycle_proteins, set1_name = "RNAse", set2_name="Dosage", set3_name="Cell cycle", subset_to=geiger_u2os_proteins)

makeVennPlot(TMT_RNAse_proteins, TMT_dosage_rep_proteins, TMT_cell_cycle_proteins, set1_name = "RNAse", set2_name="Dosage", set3_name="Cell cycle")

signal_peptides <- unique(signal_peptides_df$accession)
makeVennPlot(seen_once_proteins, signal_peptides, glycoproteins, subset_to=geiger_u2os_proteins, set2_name="Signal peptide")

makeVennPlot(seen_twice_proteins, signal_peptides, glycoproteins, subset_to=geiger_u2os_proteins, set2_name="Signal peptide")

makeVennPlot(seen_three_proteins, signal_peptides, glycoproteins, subset_to=geiger_u2os_proteins, set2_name="Signal peptide")

makeVennPlot(seen_all_proteins, signal_peptides, glycoproteins, subset_to=geiger_u2os_proteins, set2_name="Signal peptide")

evi_signal_peptides <- unique(signal_peptides_df[signal_peptides_df$evidence=="True",]$accession)
makeVennPlot(seen_once_proteins, evi_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with evidence)")

makeVennPlot(seen_twice_proteins, evi_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with evidence)")

makeVennPlot(seen_three_proteins, evi_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with evidence)")

makeVennPlot(seen_all_proteins, evi_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with evidence)")

exp_signal_peptides <- unique(signal_peptides_df[signal_peptides_df$experimental=="True",]$accession)
makeVennPlot(seen_twice_proteins, exp_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with exp. evidence)")

makeVennPlot(seen_once_proteins, exp_signal_peptides, glycoproteins,
             subset_to=geiger_u2os_proteins, set2_name="Signal peptide\n(with exp. evidence)")

agg_geiger_max$glycoprotein <- agg_geiger_max$master_protein %in% unique(glycoproteins_df$protein)
agg_geiger_max$RBP <- agg_geiger_max$master_protein %in% unique(go_RNA_binding_df$Entry)
agg_geiger_max$seen <- agg_geiger_max$master_protein %in% all_proteins
agg_geiger_max$seen_once <- agg_geiger_max$master_protein %in% names(protein_counts[protein_counts==1])
agg_geiger_max$seen_twice <- agg_geiger_max$master_protein %in% names(protein_counts[protein_counts>1])
agg_geiger_max$seen_three <- agg_geiger_max$master_protein %in% names(protein_counts[protein_counts>2])
agg_geiger_max$seen_all <- agg_geiger_max$master_protein %in% names(protein_counts[protein_counts>3])
agg_geiger_max$seen_twice_glycoproteins <- (agg_geiger_max$seen_twice & agg_geiger_max$glycoprotein)
agg_geiger_max$signal <- agg_geiger_max$master_protein %in% signal_peptides
print(table(agg_geiger_max$signal))

FALSE  TRUE 
 6909   545 

print(agg_geiger_max)

saveRDS(agg_geiger_max, "agg_geiger_max.rds")

rows <- NULL
n=1
for(localisation in c("ER", "GOLGI", "LYSOSOME", "PM")){
  if(is.na(localisation)){
    next()}
  print(localisation)
  tmp_df <- agg_geiger_max[(agg_geiger_max$glycoprotein==T & 
                            agg_geiger_max$svm==localisation),]
  tmp_df<- tmp_df[!is.na(tmp_df$master_protein),]
  
  
  print(table(tmp_df$signal, tmp_df$Freq))
  print(table(tmp_df$Freq>0))
  
  #for(freq in 1:4){ # SILAC REMOVED
  for(freq in 1:3){
    ft <- fisher.test(table(tmp_df$Freq>=freq, tmp_df$signal))
    rows[[n]]<-c(localisation, freq, ft$p.value, ft$estimate, ft$conf.int[1:2])
    n <- n+1
  }
}

[1] "ER"
       
         0  1  2  3
  FALSE 29  5  4  7
  TRUE  44  7  6 27

FALSE  TRUE 
   73    56 
[1] "GOLGI"
       
         0  1  2  3
  FALSE 28  3  1  1
  TRUE  11  1  3  3

FALSE  TRUE 
   39    12 
[1] "LYSOSOME"
       
         0  1  2  3
  FALSE  3  2  1  2
  TRUE  30  6  5  5

FALSE  TRUE 
   33    21 
[1] "PM"
       
         0  1  2  3
  FALSE 30 16  8 10
  TRUE  39 13 19 35

FALSE  TRUE 
   69   101 

final_df <- data.frame(do.call("rbind", rows))
new_colnames <- c("localisation", "freq", "p.value", "estimate", "ci_low", "ci_high")
colnames(final_df) <- new_colnames
final_df[,new_colnames[2:6]] = apply(final_df[,new_colnames[2:6]], 2, function(x) as.numeric(as.character(x)))
                  
p <- ggplot(final_df[final_df$localisation %in% c("PM", "ER"),], aes(freq, estimate, group=localisation, colour=localisation)) +
  geom_point() + geom_line() + my_theme +
  geom_line(aes(y=ci_low), colour="black", linetype=2) +
  geom_line(aes(y=ci_high), colour="black", linetype=2) +
  facet_wrap(~localisation, scales="free") +
  expand_limits(y = 0) +
  scale_colour_discrete(guide=F) +
  xlab("Protein observed in at least n experiments") +
  ylab("Signal peptide odds ratio")
print(p)

rows = NULL
n = 1
#for(freq in 1:4){
for(freq in 1:3){
  tmp_df <- agg_geiger_max[agg_geiger_max$Freq>=freq,]
  total = length(tmp_df$master_protein)
  for(annot in c("RBP", "glycoprotein", "signal")){
    obs <- sum(tmp_df[[annot]])
    exp <- sum(agg_geiger_max[[annot]]) * (total/length(agg_geiger_max$master_protein))
    over_rep <- obs/exp
    print(freq>0)
    #if(freq>0){
    ft <- fisher.test(table(agg_geiger_max$Freq>=freq, agg_geiger_max[[annot]]))
    rows[[n]]<-c(freq, annot, mean(as.numeric(tmp_df[[annot]])), exp, obs, over_rep,
                 ft$p.value, ft$estimate, ft$conf.int[1:2])
    #}
    #else{
    #  rows[[n]]<-c(freq, annot, mean(as.numeric(tmp_df[[annot]])), exp, obs, over_rep, NA, NA, NA)
    #}
    n <- n+1
}
#rows = NULL
agg_geiger_max_only_glyco <- agg_geiger_max[(agg_geiger_max$glycoprotein==T & 
                                               agg_geiger_max$svm=="PM"),]
  
#for(freq in 1:4){
for(freq in 1:3){
  tmp_df <- agg_geiger_max_only_glyco[agg_geiger_max_only_glyco$Freq>=freq,]
  total = length(tmp_df$master_protein)
  obs <- sum(tmp_df[["signal"]])
  exp <- sum(agg_geiger_max_only_glyco[["signal"]]) * (total/length(agg_geiger_max_only_glyco$master_protein))
  over_rep <- obs/exp
  if(freq>0){
    ft <- fisher.test(table(agg_geiger_max_only_glyco$Freq>=freq, agg_geiger_max_only_glyco$signal))
  
    rows[[n]]<-c(freq, "signal_glyco", mean(as.numeric(tmp_df[["signal"]])), exp, obs, over_rep,
                 ft$p.value, ft$estimate, ft$conf.int[1:2])
  }
  else{
    rows[[n]]<-c(freq, "signal_glyco", mean(as.numeric(tmp_df[["signal"]])), exp, obs, over_rep, NA, NA, NA)
    
  }
  #print(rows[[n]])
  
  print(freq)    
  print(dim(tmp_df))
  print(exp)
  print(obs)
  n <- n+1
}
    
}

[1] TRUE
[1] TRUE
[1] TRUE
[1] 1
[1] 417  19
[1] NA
[1] NA
[1] 2
[1] 388  19
[1] NA
[1] NA
[1] 3
[1] 361  19
[1] NA
[1] NA
[1] TRUE
[1] TRUE
[1] TRUE
[1] 1
[1] 417  19
[1] NA
[1] NA
[1] 2
[1] 388  19
[1] NA
[1] NA
[1] 3
[1] 361  19
[1] NA
[1] NA
[1] TRUE
[1] TRUE
[1] TRUE
[1] 1
[1] 417  19
[1] NA
[1] NA
[1] 2
[1] 388  19
[1] NA
[1] NA
[1] 3
[1] 361  19
[1] NA
[1] NA

over_rep_df <- data.frame(do.call("rbind", rows))
colnames(over_rep_df) <- c("Freq", "feature", "fraction", "exp", "obs", "over_rep",
                           "p.value", "odds_ratio", "odds_ci")
print(over_rep_df)

over_rep_df$over_rep <- as.numeric(as.character(over_rep_df$over_rep))
over_rep_df$fraction <- as.numeric(as.character(over_rep_df$fraction))
over_rep_df$Freq <- as.numeric(as.character(over_rep_df$Freq))
over_rep_df$odds_ratio <- as.numeric(as.character(over_rep_df$odds_ratio))
p <- ggplot(over_rep_df, aes(as.numeric(Freq), over_rep, colour=feature)) +
  geom_line() + my_theme
print(p)

p <- ggplot(over_rep_df, aes(as.numeric(Freq), fraction, colour=feature)) +
  geom_line() + my_theme
print(p)

p <- ggplot(over_rep_df[over_rep_df$Freq>0,], aes(as.numeric(Freq), odds_ratio, colour=feature)) +
  geom_point() +  geom_line() + my_theme + expand_limits(y = 0)
print(p)

p <- ggplot(over_rep_df[(over_rep_df$Freq>0 & over_rep_df$feature %in% c("RBP", "glycoprotein")),],
            aes(as.numeric(Freq), odds_ratio, colour=feature)) +
  geom_point() +  geom_line() + my_theme + expand_limits(y = 0) +
  xlab("Protein observed in at least n experiments") +
  ylab("Odds ratio")
print(p)

runFishersEnrichment(agg_geiger_max, "RBP", "seen_once")

       
        FALSE TRUE
  FALSE  5520  604
  TRUE   1206  124

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.5753
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.760614 1.153889
sample estimates:
odds ratio 
 0.9396978 

runFishersEnrichment(agg_geiger_max, "RBP", "seen_twice")

       
        FALSE TRUE
  FALSE  4739 1385
  TRUE    574  756

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 3.973062 5.111818
sample estimates:
odds ratio 
  4.505475 

runFishersEnrichment(agg_geiger_max, "RBP", "seen_three")

       
        FALSE TRUE
  FALSE  5146  978
  TRUE    690  640

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 4.287087 5.553530
sample estimates:
odds ratio 
  4.879162 

runFishersEnrichment(agg_geiger_max, "glycoprotein", "seen_once")

       
        FALSE TRUE
  FALSE  6064  632
  TRUE    662   96

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.00658
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 1.094364 1.754705
sample estimates:
odds ratio 
   1.39134 

runFishersEnrichment(agg_geiger_max, "glycoprotein", "seen_twice")

       
        FALSE TRUE
  FALSE  4768 1928
  TRUE    545  213

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.7033
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8138505 1.1448169
sample estimates:
odds ratio 
 0.9665266 

runFishersEnrichment(agg_geiger_max, "glycoprotein", "seen_three")

       
        FALSE TRUE
  FALSE  5227 1469
  TRUE    609  149

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.1631
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.7161606 1.0532736
sample estimates:
odds ratio 
 0.8705805 

runFishersEnrichment(agg_geiger_max[agg_geiger_max$glycoprotein,], "seen_once", "signal")

       
        FALSE TRUE
  FALSE   277  385
  TRUE     45   51

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.3775
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.5189606 1.2851499
sample estimates:
odds ratio 
 0.8156389 

runFishersEnrichment(agg_geiger_max[agg_geiger_max$glycoprotein,], "seen_twice", "signal")

       
        FALSE TRUE
  FALSE   255  290
  TRUE     67  146

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.00012
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 1.355145 2.722745
sample estimates:
odds ratio 
  1.914511 

runFishersEnrichment(agg_geiger_max[agg_geiger_max$glycoprotein,], "seen_three", "signal")

       
        FALSE TRUE
  FALSE   276  333
  TRUE     46  103

    Fisher's Exact Test for Count Data

data:  table(df[[col]], df[[identified_col]])
p-value = 0.001612
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 1.248474 2.785477
sample estimates:
odds ratio 
  1.854374 

qm <- myProtMapper(union(all_proteins, unique(agg_geiger_max$master_protein)))

Querying chunk 1
Querying chunk 2
Querying chunk 3
Querying chunk 4
Querying chunk 5
Querying chunk 6
Querying chunk 7
Querying chunk 8

Finished
Pass returnall=TRUE to return lists of duplicate or missing query terms.
[1] "No KEGG"

the condition has length > 1 and only the first element will be used

# Mapping Uniprot to GO or Uniprot to Interpro for goseq
uniprot.go <- makeGene2Cat(qm,"query","go.all",";")
uniprot.doms <- makeGene2Cat(qm,"query","domains",";")

all_pwf <- makePWF(agg_geiger_max, "seen", "harm_mean_bias", "master_protein")

[1] 2869

initial point very close to some inequality constraints

makePWFPlot(all_pwf, xlab="U2OS abundance")

go_all <- getEnrichedGO(all_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 92 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

print(go_all)

plotGOTerms(go_all, sum(agg_geiger_max$seen),
            length(agg_geiger_max$harm_mean_bias), numObs_filter=10, 
            enrichment_filter=0, switch_axes=T, BH_filter=0.01)

$p
$p$MF

$p$CC

$p$BP


$g

NA

agg_geiger_max$novel <- (agg_geiger_max$Freq==3 & agg_geiger_max$RBP == FALSE)
novel_pwf <- makePWF(agg_geiger_max[agg_geiger_max$Freq==3,], "novel", "harm_mean_bias", "master_protein")

[1] 978

initial point very close to some inequality constraints

makePWFPlot(novel_pwf, xlab="U2OS abundance")

go_novel <- getEnrichedGO(novel_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 4 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

print(table(agg_geiger_max[agg_geiger_max$Freq==3,"novel"]))

FALSE  TRUE 
  640   978 

plotGOTerms(go_novel, sum(agg_geiger_max$seen),
            length(agg_geiger_max$harm_mean_bias), numObs_filter=10, 
            enrichment_filter=0, switch_axes=T, BH_filter=0.01)

$p
$p$all


$g

NA

SRP_targetting <- uniprot.go[uniprot.go$to.id=="GO:0006614", "query"]
print(length(intersect(agg_geiger_max[agg_geiger_max$glycoprotein==T, "master_protein"], SRP_targetting)))

[1] 0

print(length(intersect(agg_geiger_max[agg_geiger_max$signal==T, "master_protein"], SRP_targetting)))

[1] 0

twice_pwf <- makePWF(agg_geiger_max, "seen_twice", "harm_mean_bias", "master_protein")

[1] 2141

initial point very close to some inequality constraints

makePWFPlot(twice_pwf, xlab="U2OS abundance")

go_twice <- getEnrichedGO(twice_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 92 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

go_twice <- plotGOTerms(go_twice, sum(agg_geiger_max$seen_twice), length(agg_geiger_max$harm_mean_bias), 
                        numObs_filter=10, enrichment_filter=-Inf, switch_axes=T, BH_filter=0.01)
print(go_twice$p)

$MF

$CC

$BP

plotGOTerms

function(GO_df, len_foreground, len_background,
                        BH_filter=0.01, enrichment_filter=2, numObs_filter=50,
                        switch_axes=F, plot_top=10, term.col="term", cut_at){
  
  # GO_df = dataframe from call to goseq
  # len_foreground = total number of proteins in foreground
  # len_background = total number of proteins in background
  
  GO_df$BH <-  p.adjust(GO_df$over_represented_pvalue, method="BH")
  GO_df$BH[GO_df$BH==0] <- 1E-16
  GO_df$enrichment <- log((GO_df$numDEInCat/GO_df$numInCat) / (len_foreground/len_background),2)
  
  GO_filtered_df <- GO_df[GO_df$BH < BH_filter,]
  GO_filtered_df <- GO_filtered_df[GO_filtered_df$enrichment > enrichment_filter,]
  GO_filtered_df <- GO_filtered_df[GO_filtered_df$numDEInCat > numObs_filter,]
  
  if(switch_axes){ # determine how long to allow GO term desc. before truncating
    GO_filtered_df <- GO_filtered_df[order(GO_filtered_df$enrichment),]
    if(missing(cut_at)){
      cut_at <- 40
    }
  }
  else{
    GO_filtered_df <- GO_filtered_df[order(-GO_filtered_df$enrichment),]
    if(missing(cut_at)){
      cut_at <- 25
    }
  }
  
  GO_filtered_df$term <- factor(GO_filtered_df[,term.col], levels=unique(GO_filtered_df[,term.col]))
  
  # ------------------------
  # Function\t: shortenTerm
  # ------------------------
  shortenTerm <- function(term, cut_at){
    if(nchar(term)>cut_at){
      return(paste0(substr(term, 1, cut_at), " [..]"))
    }
    else{
      return(term)
    }
  }
  
  plots = NULL
  
  if(length(GO_filtered_df$ontology)<=plot_top){
    GO_filtered_df <- GO_filtered_df[order(GO_filtered_df$ontology),]
    p <- ggplot(GO_filtered_df, aes(interaction(term, ontology), enrichment, fill=log(BH,10))) +
      geom_bar(stat="identity") + 
      xlab("") + ylab("Enrichment (Log2)") +
      scale_fill_continuous(name="BH adj. p-value\\n(Log 10)\\n", low="skyblue", high="grey30") +
      my_theme +
      theme(
        text=element_text(size=15),
        plot.title=element_text(hjust=0.5)) +
      scale_x_discrete(labels=paste0(sapply(as.character(GO_filtered_df[[term.col]]), FUN=function(x) shortenTerm(x, cut_at)),
                                     " (", GO_filtered_df$ontology, ")"))
    
    if(switch_axes){
      p <- p + coord_flip()
    }
    else{
      p <- p + theme(axis.text.x=element_text(size=12, angle=45, vjust=1, hjust=1))
    }
    
    plots[["all"]] <- p
  }
  else{
    for(onto_class in unique(GO_filtered_df$ontology)){
      tmp_df <- GO_filtered_df[GO_filtered_df$ontology == onto_class,]
      
      if(switch_axes){
        tmp_df <- tail(tmp_df,min(plot_top, length(tmp_df[,1])))
      }
      else{
        tmp_df <- head(tmp_df,min(plot_top, length(tmp_df[,1])))
      }
      
      tmp_df$short_term <- sapply(as.character(tmp_df$term), FUN=function(x) shortenTerm(x, cut_at))
      
      p <- ggplot(tmp_df, aes(term, enrichment, fill=log(BH,10))) +
        geom_bar(stat="identity") + 
        xlab("") + ylab("Enrichment (Log2)") +
        scale_fill_continuous(name="BH adj. p-value\\n(Log 10)\\n", low="skyblue", high="grey30") +
        ggtitle(onto_class) +
        my_theme +
        theme(
          text=element_text(size=15),
          plot.title=element_text(hjust=0.5)) +
        scale_x_discrete(labels=tmp_df$short_term)
      
      if(switch_axes){
        p <- p + coord_flip()
      }
      else{
        p <- p + theme(axis.text.x=element_text(size=12, angle=45, vjust=1, hjust=1))
      }
      plots[[onto_class]] <- p
    }
  }
  return(list(p=plots,g=GO_df))
}
<bytecode: 0x2e1523a8>

three_pwf <- makePWF(agg_geiger_max, "seen_three", "harm_mean_bias", "master_protein")

[1] 1618

initial point very close to some inequality constraints

makePWFPlot(twice_pwf, xlab="U2OS abundance")

go_three <- getEnrichedGO(three_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 92 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

go_three <- plotGOTerms(go_three, sum(agg_geiger_max$seen_three), length(agg_geiger_max$harm_mean_bias), 
                        numObs_filter=10, enrichment_filter=-Inf, switch_axes=T, BH_filter=0.01)
print(go_twice$p)

$MF

$CC

$BP

once_pwf <- makePWF(agg_geiger_max, "seen_once", "harm_mean_bias", "master_protein")

[1] 728

initial point very close to some inequality constraints

makePWFPlot(once_pwf, xlab="U2OS abundance")

go_once <- getEnrichedGO(once_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 92 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

go_once <- plotGOTerms(go_once, sum(agg_geiger_max$seen_once), length(agg_geiger_max$harm_mean_bias),
                       numObs_filter=10,  enrichment_filter=-Inf, switch_axes=T, BH_filter=0.01)
print(go_once$p)

$all

domain_twice.abundance <- goseq(twice_pwf, gene2cat=uniprot.doms)

Using manually entered categories.
For 114 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...

domain_twice.abundance$BH <-  p.adjust(domain_twice.abundance$over_represented_pvalue, method="BH")
print(head(domain_twice.abundance))

domain_once.abundance <- goseq(once_pwf, gene2cat=uniprot.doms)

Using manually entered categories.
For 114 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...

domain_once.abundance$BH <-  p.adjust(domain_once.abundance$over_represented_pvalue, method="BH")
print(head(domain_once.abundance))

go_merged <- merge(go_three$g[,c("category", "term", "over_represented_pvalue", "enrichment")],
                   go_once$g[,c("category", "term", "over_represented_pvalue", "enrichment")],
                   by="category")
sig_MF_terms <- go_three$g[(go_three$g$BH<0.01 & go_three$g$ontology=="MF"), "term"]
go_merged$sig_MF_term <- go_merged$term.x %in% sig_MF_terms
go_merged$label <- go_merged$term.x
go_merged$label[go_merged$sig_MF_term==F] <- NA
p <- ggplot(go_merged[go_merged$category %in% go_twice$g[go_three$g$BH<0.01,"category"],],
            aes(log(over_represented_pvalue.x,10), log(over_represented_pvalue.y,10))) +
  geom_point() + geom_smooth(method="lm") + my_theme
print(p)

p <- ggplot(go_merged[(go_merged$category %in% go_three$g[go_three$g$BH<0.01,"category"] &
                         go_merged$enrichment.x > 0),],
            aes(enrichment.x, enrichment.y)) +
  geom_point(aes(colour=sig_MF_term)) + geom_smooth(method="lm") +
  geom_text(aes(label=label), nudge_x = -0.2, nudge_y = 0.3, colour="red",
            check_overlap = TRUE, hjust = 1, size=3.4) +
  scale_colour_manual(values=c("black", "red"), guide=F) +
  my_theme
print(p)

twice_glyco_pwf <- makePWF(agg_geiger_max, "seen_twice_glycoproteins", "harm_mean_bias", "master_protein")

[1] 213

initial point very close to some inequality constraints

makePWFPlot(twice_glyco_pwf, xlab="U2OS abundance")

go_twice_glyco <- getEnrichedGO(twice_glyco_pwf, gene2cat=uniprot.go)

Using manually entered categories.
For 92 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

go_twice_glyco <- plotGOTerms(go_twice_glyco, sum(agg_geiger_max$seen_twice_glycoproteins),
                              length(agg_geiger_max$harm_mean_bias), 
                              numObs_filter=10, enrichment_filter=1, switch_axes=T, BH_filter=0.01)
print(go_twice_glyco$p)

$CC

$MF

$BP

protein_desc <- read.csv("../../../shared_files/human_protein_ids.tsv", sep="\t", header=F)
colnames(protein_desc) <- c("UniprotID", "Symbol", "Description")
agg_geiger_max <- merge(agg_geiger_max, protein_desc, by.x="master_protein", by.y="UniprotID", all.x=T)

SRP_targetting <- uniprot.go[uniprot.go$to.id=="GO:0006614", "query"]
tmp_df <- agg_geiger_max[agg_geiger_max$master_protein %in% SRP_targetting,]
tmp_df <- tmp_df[order(-tmp_df$Freq),]
print(tmp_df)

print(tmp_df[,c("Freq", "Description", "svm", "svm.scores", "Length")])

print(tmp_df[tmp_df$Freq>0,"Description"])

 [1] Signal recognition particle subunit SRP72 (SRP72) (Signal recognition particle 72 kDa protein)                                                                                                                                                                                                                                                                         
 [2] 60S acidic ribosomal protein P2 (Large ribosomal subunit protein P2) (Renal carcinoma antigen NY-REN-44)                                                                                                                                                                                                                                                               
 [3] 60S acidic ribosomal protein P0 (60S ribosomal protein L10E) (Large ribosomal subunit protein uL10)                                                                                                                                                                                                                                                                    
 [4] Signal recognition particle receptor subunit alpha (SR-alpha) (Docking protein alpha) (DP-alpha)                                                                                                                                                                                                                                                                       
 [5] 40S ribosomal protein S2 (40S ribosomal protein S4) (Protein LLRep3) (Small ribosomal subunit protein uS5)                                                                                                                                                                                                                                                             
 [6] 60S ribosomal protein L7 (Large ribosomal subunit protein uL30)                                                                                                                                                                                                                                                                                                        
 [7] 40S ribosomal protein S3 (EC 4.2.99.18) (Small ribosomal subunit protein uS3)                                                                                                                                                                                                                                                                                          
 [8] 40S ribosomal protein S12 (Small ribosomal subunit protein eS12)                                                                                                                                                                                                                                                                                                       
 [9] 60S ribosomal protein L13 (Breast basic conserved protein 1) (Large ribosomal subunit protein eL13)                                                                                                                                                                                                                                                                    
[10] 60S ribosomal protein L10 (Laminin receptor homolog) (Large ribosomal subunit protein uL16) (Protein QM) (Ribosomal protein L10) (Tumor suppressor QM)                                                                                                                                                                                                                 
[11] 60S ribosomal protein L12 (Large ribosomal subunit protein uL11)                                                                                                                                                                                                                                                                                                       
[12] 60S ribosomal protein L22 (EBER-associated protein) (EAP) (Epstein-Barr virus small RNA-associated protein) (Heparin-binding protein HBp15) (Large ribosomal subunit protein eL22)                                                                                                                                                                                     
[13] 60S ribosomal protein L4 (60S ribosomal protein L1) (Large ribosomal subunit protein uL4)                                                                                                                                                                                                                                                                              
[14] 40S ribosomal protein S19 (Small ribosomal subunit protein eS19)                                                                                                                                                                                                                                                                                                       
[15] 60S ribosomal protein L3 (HIV-1 TAR RNA-binding protein B) (TARBP-B) (Large ribosomal subunit protein uL3)                                                                                                                                                                                                                                                             
[16] 60S ribosomal protein L35 (Large ribosomal subunit protein uL29)                                                                                                                                                                                                                                                                                                       
[17] 60S ribosomal protein L27a (Large ribosomal subunit protein uL15)                                                                                                                                                                                                                                                                                                      
[18] 60S ribosomal protein L5 (Large ribosomal subunit protein uL18)                                                                                                                                                                                                                                                                                                        
[19] 60S ribosomal protein L21 (Large ribosomal subunit protein eL21)                                                                                                                                                                                                                                                                                                       
[20] 60S ribosomal protein L28 (Large ribosomal subunit protein eL28)                                                                                                                                                                                                                                                                                                       
[21] 40S ribosomal protein S9 (Small ribosomal subunit protein uS4)                                                                                                                                                                                                                                                                                                         
[22] 40S ribosomal protein S10 (Small ribosomal subunit protein eS10)                                                                                                                                                                                                                                                                                                       
[23] 60S ribosomal protein L29 (Cell surface heparin-binding protein HIP) (Large ribosomal subunit protein eL29)                                                                                                                                                                                                                                                            
[24] 60S ribosomal protein L34 (Large ribosomal subunit protein eL34)                                                                                                                                                                                                                                                                                                       
[25] 60S ribosomal protein L14 (CAG-ISL 7) (Large ribosomal subunit protein eL14)                                                                                                                                                                                                                                                                                           
[26] 40S ribosomal protein S20 (Small ribosomal subunit protein uS10)                                                                                                                                                                                                                                                                                                       
[27] Signal recognition particle 54 kDa protein (SRP54)                                                                                                                                                                                                                                                                                                                     
[28] 40S ribosomal protein S3a (Small ribosomal subunit protein eS1) (v-fos transformation effector protein) (Fte-1)                                                                                                                                                                                                                                                        
[29] 60S ribosomal protein L26 (Large ribosomal subunit protein uL24)                                                                                                                                                                                                                                                                                                       
[30] 60S ribosomal protein L15 (Large ribosomal subunit protein eL15)                                                                                                                                                                                                                                                                                                       
[31] 60S ribosomal protein L37 (G1.16) (Large ribosomal subunit protein eL37)                                                                                                                                                                                                                                                                                               
[32] 40S ribosomal protein S7 (Small ribosomal subunit protein eS7)                                                                                                                                                                                                                                                                                                         
[33] 40S ribosomal protein S8 (Small ribosomal subunit protein eS8)                                                                                                                                                                                                                                                                                                         
[34] 40S ribosomal protein S15a (Small ribosomal subunit protein uS8)                                                                                                                                                                                                                                                                                                       
[35] 40S ribosomal protein S16 (Small ribosomal subunit protein uS9)                                                                                                                                                                                                                                                                                                        
[36] 40S ribosomal protein S14 (Small ribosomal subunit protein uS11)                                                                                                                                                                                                                                                                                                       
[37] 40S ribosomal protein S23 (Small ribosomal subunit protein uS12)                                                                                                                                                                                                                                                                                                       
[38] 40S ribosomal protein S18 (Ke-3) (Ke3) (Small ribosomal subunit protein uS13)                                                                                                                                                                                                                                                                                          
[39] 40S ribosomal protein S13 (Small ribosomal subunit protein uS15)                                                                                                                                                                                                                                                                                                       
[40] 40S ribosomal protein S11 (Small ribosomal subunit protein uS17)                                                                                                                                                                                                                                                                                                       
[41] 60S ribosomal protein L7a (Large ribosomal subunit protein eL8) (PLA-X polypeptide) (Surfeit locus protein 3)                                                                                                                                                                                                                                                          
[42] 40S ribosomal protein S4, X isoform (SCR10) (Single copy abundant mRNA protein) (Small ribosomal subunit protein eS4)                                                                                                                                                                                                                                                  
[43] 40S ribosomal protein S6 (Phosphoprotein NP33) (Small ribosomal subunit protein eS6)                                                                                                                                                                                                                                                                                   
[44] 60S ribosomal protein L23 (60S ribosomal protein L17) (Large ribosomal subunit protein uL14)                                                                                                                                                                                                                                                                           
[45] 40S ribosomal protein S24 (Small ribosomal subunit protein eS24)                                                                                                                                                                                                                                                                                                       
[46] 60S ribosomal protein L30 (Large ribosomal subunit protein eL30)                                                                                                                                                                                                                                                                                                       
[47] 60S ribosomal protein L31 (Large ribosomal subunit protein eL31)                                                                                                                                                                                                                                                                                                       
[48] 60S ribosomal protein L10a (CSA-19) (Large ribosomal subunit protein uL1) (Neural precursor cell expressed developmentally down-regulated protein 6) (NEDD-6)                                                                                                                                                                                                          
[49] 60S ribosomal protein L11 (CLL-associated antigen KW-12) (Large ribosomal subunit protein uL5)                                                                                                                                                                                                                                                                         
[50] 60S ribosomal protein L8 (Large ribosomal subunit protein uL2)                                                                                                                                                                                                                                                                                                         
[51] 60S ribosomal protein L24 (60S ribosomal protein L30) (Large ribosomal subunit protein eL24)                                                                                                                                                                                                                                                                           
[52] 60S ribosomal protein L19 (Large ribosomal subunit protein eL19)                                                                                                                                                                                                                                                                                                       
[53] 60S ribosomal protein L18a (Large ribosomal subunit protein eL20)                                                                                                                                                                                                                                                                                                      
[54] 60S ribosomal protein L6 (Large ribosomal subunit protein eL6) (Neoplasm-related protein C140) (Tax-responsive enhancer element-binding protein 107) (TaxREB107)                                                                                                                                                                                                       
[55] Translocation protein SEC63 homolog                                                                                                                                                                                                                                                                                                                                    
[56] Signal recognition particle subunit SRP68 (SRP68) (Signal recognition particle 68 kDa protein)                                                                                                                                                                                                                                                                         
[57] 60S ribosomal protein L27 (Large ribosomal subunit protein eL27)                                                                                                                                                                                                                                                                                                       
[58] 60S ribosomal protein L23a (Large ribosomal subunit protein uL23)                                                                                                                                                                                                                                                                                                      
[59] 40S ribosomal protein S26 (Small ribosomal subunit protein eS26)                                                                                                                                                                                                                                                                                                       
[60] 60S ribosomal protein L36 (Large ribosomal subunit protein eL36)                                                                                                                                                                                                                                                                                                       
[61] 40S ribosomal protein SA (37 kDa laminin receptor precursor) (37LRP) (37/67 kDa laminin receptor) (LRP/LR) (67 kDa laminin receptor) (67LR) (Colon carcinoma laminin-binding protein) (Laminin receptor 1) (LamR) (Laminin-binding protein precursor p40) (LBP/p40) (Multidrug resistance-associated protein MGr1-Ag) (NEM/1CHD4) (Small ribosomal subunit protein uS2)
[62] 40S ribosomal protein S5 (Small ribosomal subunit protein uS7) [Cleaved into: 40S ribosomal protein S5, N-terminally processed]                                                                                                                                                                                                                                        
[63] 40S ribosomal protein S25 (Small ribosomal subunit protein eS25)                                                                                                                                                                                                                                                                                                       
[64] 40S ribosomal protein S28 (Small ribosomal subunit protein eS28)                                                                                                                                                                                                                                                                                                       
[65] Ubiquitin-40S ribosomal protein S27a (Ubiquitin carboxyl extension protein 80) [Cleaved into: Ubiquitin; 40S ribosomal protein S27a (Small ribosomal subunit protein eS31)]                                                                                                                                                                                            
20244 Levels: (E3-independent) E2 ubiquitin-conjugating enzyme (EC 2.3.2.24) (E2/E3 hybrid ubiquitin-protein ligase UBE2O) (Ubiquitin carrier protein O) (Ubiquitin-conjugating enzyme E2 O) (Ubiquitin-conjugating enzyme E2 of 230 kDa) (Ubiquitin-conjugating enzyme E2-230K) (Ubiquitin-protein ligase O) ...

print(tmp_df[tmp_df$Freq==0,"Description"])

 [1] 60S acidic ribosomal protein P1 (Large ribosomal subunit protein P1)                                                                                                                               
 [2] 40S ribosomal protein S17 (Small ribosomal subunit protein eS17)                                                                                                                                   
 [3] Signal recognition particle 19 kDa protein (SRP19)                                                                                                                                                 
 [4] 60S ribosomal protein L35a (Cell growth-inhibiting gene 33 protein) (Large ribosomal subunit protein eL33)                                                                                         
 [5] 60S ribosomal protein L17 (60S ribosomal protein L23) (Large ribosomal subunit protein uL22) (PD-1)                                                                                                
 [6] 60S ribosomal protein L9 (Large ribosomal subunit protein uL6)                                                                                                                                     
 [7] Signal recognition particle 14 kDa protein (SRP14) (18 kDa Alu RNA-binding protein)                                                                                                                
 [8] 60S ribosomal protein L13a (23 kDa highly basic protein) (Large ribosomal subunit protein uL13)                                                                                                    
 [9] Signal recognition particle 9 kDa protein (SRP9)                                                                                                                                                   
[10] 60S ribosomal protein L37a (Large ribosomal subunit protein eL43)                                                                                                                                  
[11] Protein transport protein Sec61 subunit alpha isoform 1 (Sec61 alpha-1)                                                                                                                            
[12] 40S ribosomal protein S29 (Small ribosomal subunit protein uS14)                                                                                                                                   
[13] 40S ribosomal protein S15 (RIG protein) (Small ribosomal subunit protein uS19)                                                                                                                     
[14] 60S ribosomal protein L32 (Large ribosomal subunit protein eL32)                                                                                                                                   
[15] Ubiquitin-60S ribosomal protein L40 (CEP52) (Ubiquitin A-52 residue ribosomal protein fusion product 1) [Cleaved into: Ubiquitin; 60S ribosomal protein L40 (Large ribosomal subunit protein eL40)]
[16] 60S ribosomal protein L38 (Large ribosomal subunit protein eL38)                                                                                                                                   
[17] 40S ribosomal protein S21 (Small ribosomal subunit protein eS21)                                                                                                                                   
[18] 60S ribosomal protein L36a (60S ribosomal protein L44) (Cell growth-inhibiting gene 15 protein) (Cell migration-inducing gene 6 protein) (Large ribosomal subunit protein eL42)                    
[19] 60S ribosomal protein L18 (Large ribosomal subunit protein eL18)                                                                                                                                   
[20] Translocon-associated protein subunit gamma (TRAP-gamma) (Signal sequence receptor subunit gamma) (SSR-gamma)                                                                                      
20244 Levels: (E3-independent) E2 ubiquitin-conjugating enzyme (EC 2.3.2.24) (E2/E3 hybrid ubiquitin-protein ligase UBE2O) (Ubiquitin carrier protein O) (Ubiquitin-conjugating enzyme E2 O) (Ubiquitin-conjugating enzyme E2 of 230 kDa) (Ubiquitin-conjugating enzyme E2-230K) (Ubiquitin-protein ligase O) ...

print(tmp_df[grep("Signal", tmp_df$Description),c("master_protein", "Freq", "Description", "svm", "svm.scores", "Length")])

tmp_df <- agg_geiger_max[(#agg_geiger_max$glycoprotein==T &
                            #agg_geiger_max$seen_all==T &
                            agg_geiger_max$signal==T &
                            agg_geiger_max$svm=="PM" &
                            agg_geiger_max$svm.scores>0.9),]
tmp_df <- tmp_df[!is.na(tmp_df$master_protein),]
tmp_df[order(tmp_df$Length),]